General information for g7193.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Polyadenylate-binding protein 2.
Parent gene
- The parent gene g7193 is located on chr_2: 22029874..22031157 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_2 | g7193 | g7193.t17 | TSS | g7193.t17 | 22029455 | 22029455 |
| chr_2 | g7193 | g7193.t17 | isoform | g7193.t17 | 22029527 | 22031157 |
| chr_2 | g7193 | g7193.t17 | exon | g7193.t17.exon1 | 22029527 | 22029529 |
| chr_2 | g7193 | g7193.t17 | exon | g7193.t17.exon2 | 22029816 | 22030415 |
| chr_2 | g7193 | g7193.t17 | cds | g7193.t17.CDS1 | 22029889 | 22030415 |
| chr_2 | g7193 | g7193.t17 | exon | g7193.t17.exon3 | 22030469 | 22030598 |
| chr_2 | g7193 | g7193.t17 | cds | g7193.t17.CDS2 | 22030469 | 22030511 |
| chr_2 | g7193 | g7193.t17 | exon | g7193.t17.exon4 | 22030882 | 22031157 |
| chr_2 | g7193 | g7193.t17 | TTS | g7193.t17 | 22031156 | 22031156 |
Sequences
>g7193.t17 Gene=g7193 Length=1009
AAGAAGTAAGTAAATGAACTTAATATGTTAAATGATTAATTTATTAAAAAAATAAAATTA
AAAGGAAGAGTCTGGAATGCAGATAGATCCAGAATTGGAGGCAATTAAGGCAAGAGTTAA
AGAAATGGAAGAAGAAGCAGAGAAACTTAAGCAGCTACAATCAGAAGTTAATAAGCAAAT
GACCTTAGGTAGTCCCACTTCGAGTACACCCGCTTTATCAGTTGAAGAGAAAATGGAGAT
TGACAATCGTTCTATATATGTTGGAAATGTTGATTATGGGGCCACAGCTGAAGAGCTAGA
AGCCCATTTTCACGGTTGTGGTAGCATAAATCGCGTAACGATTTTATGTAACAAAATAGA
TGGACATCCTAAGGGTTTTGCTTACATTGAATTTGCATCAAAGGACTTTGTTGAGACAGC
ATTAGCAATGAATGAGACTCTGTTTAGAGGACGTCAAATAAAAGTCATGTCCAAGAGGAC
CAACAGACCAGGACTTTGCGTTACTAATAGAATTCCCAGAGGTATGAGAGGAAGAGGATT
ATCAAGAGGACGAGCTTCTTGTTGTCACACTGGCCATCGAGGTGGACGAGCTTCACGTGC
TATGGGATACCGAGGACGTGGGATGAATTACTACTCACCTTATTAGAAAGAAAACAAAAT
TCATCAGTCAATGCAAACGTTTTCTTAGTCTTATAAGCATTTTTTACCATCATAATTTTC
CTTTAATTACTAGATAAAAAAAATAAAAGAAAAAATGATTTATTCAAAAAACATTATTTT
GCTGCTCCGACGATTTTGAAAAAAAAAGGAAGTTTCAAATCAAAAAAAAAATATATATGT
GGATTGAAGCGTTAAAAGAAAGACATTCATTATGATTTGTTTTACTCACTACAAATAATG
TTTTTTGACATTACACAAAATTTACACAATAGCATAAAACAATCTATCAATCCAATCAAG
ATGAAAAAAGGACAAAAGATTTCAACAGAAGAAGAAAATTCCAAATCCA
>g7193.t17 Gene=g7193 Length=189
MQIDPELEAIKARVKEMEEEAEKLKQLQSEVNKQMTLGSPTSSTPALSVEEKMEIDNRSI
YVGNVDYGATAEELEAHFHGCGSINRVTILCNKIDGHPKGFAYIEFASKDFVETALAMNE
TLFRGRQIKVMSKRTNRPGLCVTNRIPRGMRGRGLSRGRASCCHTGHRGGRASRAMGYRG
RGMNYYSPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g7193.t17 | CDD | cd12550 | RRM_II_PABPN1 | 59 | 134 | 2.64046E-54 |
| 6 | g7193.t17 | Coils | Coil | Coil | 7 | 37 | - |
| 5 | g7193.t17 | Gene3D | G3DSA:3.30.70.330 | - | 52 | 139 | 3.4E-25 |
| 2 | g7193.t17 | PANTHER | PTHR23236 | EUKARYOTIC TRANSLATION INITIATION FACTOR 4B/4H | 4 | 177 | 3.9E-76 |
| 3 | g7193.t17 | PANTHER | PTHR23236:SF21 | PABPN1 PROTEIN-RELATED | 4 | 177 | 3.9E-76 |
| 1 | g7193.t17 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 60 | 129 | 4.4E-17 |
| 9 | g7193.t17 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 58 | 135 | 15.596 |
| 8 | g7193.t17 | SMART | SM00360 | rrm1_1 | 59 | 131 | 1.8E-18 |
| 4 | g7193.t17 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 44 | 160 | 7.66E-28 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14396 (polyadenylate-binding protein 2)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
